ncs_mdes 0.12.0 → 0.13.0

data/lib/ncs_navigator/mdes/source_documents.rb

@@ -61,6 +61,8 @@ module NcsNavigator::Mdes
           create('3.1', '3.1/NCS_Transmission_Schema_3.1.01.00.xsd', '3.1.01.00')
         when '3.2'
           create('3.2', '3.2/NCS_Transmission_Schema_3.2.00.00.xsd', '3.2.00.00')
+        when '3.3'
+          create('3.3', '3.3/NCS_Transmission_Schema_3.3.00.00.xsd', '3.3.00.00')
         else
           raise "MDES #{version} is not supported by this version of ncs_mdes"
         end

data/lib/ncs_navigator/mdes/specification.rb

@@ -83,7 +83,7 @@ module NcsNavigator::Mdes
         '//xs:element[@name="transmission_tables"]/xs:complexType/xs:sequence/xs:element',
         source_documents.xmlns
       ).collect { |table_elt|
-        TransmissionTable.from_element(table_elt, :log => @log)
+        TransmissionTable.from_element(table_elt, :log => @log, :heuristic_overrides => heuristic_overrides)
       }.tap { |tables|
         tables.each { |t| t.variables.each { |v| v.resolve_type!(types, :log => @log) } }
         # All types must be resolved before doing FK resolution or
@@ -165,7 +165,7 @@ module NcsNavigator::Mdes
 
     def read_types
       xsd.xpath('//xs:simpleType[@name]', source_documents.xmlns).collect do |type_elt|
-        VariableType.from_xsd_simple_type(type_elt, :log => @log)
+        VariableType.from_xsd_simple_type(type_elt, :log => @log, :heuristic_overrides => heuristic_overrides)
       end
     end
     private :read_types

data/lib/ncs_navigator/mdes/transmission_table.rb

@@ -12,9 +12,13 @@ module NcsNavigator::Mdes
       log = options[:log] || NcsNavigator::Mdes.default_logger
 
       new(element['name']).tap do |table|
+        opts = options.merge({
+          :log => log,
+          :current_table_name => table.name
+        })
         table.variables = element.
           xpath('xs:complexType/xs:sequence/xs:element', SourceDocuments.xmlns).
-          collect { |col_elt| Variable.from_element(col_elt, options) }
+          collect { |col_elt| Variable.from_element(col_elt, opts) }
       end
     end
 
@@ -171,5 +175,24 @@ module NcsNavigator::Mdes
     def diff(other_table, options={})
       Differences::Entry.compute(self, other_table, DIFF_CRITERIA, options)
     end
+
+    ##
+    # This method allows for a table to have a multiple column PK. At this
+    # writing there are not any, so this is out of an abundance of caution.
+    #
+    # @return [Array<Variable>] the variables comprising the PK for this table,
+    #   or an empty array if they can't be determined.
+    def primary_key_variables
+      pks = variables.select { |v| v.type.name == 'primaryKeyType' }
+      if !pks.empty?
+        pks
+      elsif name == 'study_center'
+        variables.select { |v| v.name == 'sc_id' }
+      elsif name == 'psu'
+        variables.select { |v| v.name == 'psu_id' }
+      else
+        []
+      end
+    end
   end
 end

data/lib/ncs_navigator/mdes/variable.rb

@@ -90,21 +90,40 @@ module NcsNavigator::Mdes
             when '4'; :retired;
             else element['ncsdoc:status'];
             end
-          var.type =
-            if element['type']
-              if element['type'] =~ /^xs:/
-                VariableType.xml_schema_type(element['type'].sub(/^xs:/, ''))
-              else
-                VariableType.reference(element['type'])
-              end
-            elsif element.elements.collect { |e| e.name } == %w(simpleType)
-              VariableType.from_xsd_simple_type(element.elements.first, options)
-            else
-              log.warn("Could not determine a type for variable #{var.name.inspect} on line #{element.line}")
-              nil
-            end
+          var.type = type_for(element, var.name, log, options)
+        end
+      end
+
+      def type_for(element, name, log, options)
+        variable_type_override = deep_key_or_nil(
+          options, :heuristic_overrides, 'variable_type_references', options[:current_table_name], name)
+
+        named_type = variable_type_override || element['type']
+
+        if named_type
+          if named_type =~ /^xs:/
+            VariableType.xml_schema_type(named_type.sub(/^xs:/, ''))
+          else
+            VariableType.reference(named_type)
+          end
+        elsif element.elements.collect { |e| e.name } == %w(simpleType)
+          VariableType.from_xsd_simple_type(element.elements.first, options)
+        else
+          log.warn("Could not determine a type for variable #{name.inspect} on line #{element.line}")
+          nil
+        end
+      end
+      private :type_for
+
+      def deep_key_or_nil(h, *keys)
+        value = h[keys.shift]
+        if value.respond_to?(:[]) && !keys.empty?
+          deep_key_or_nil(value, *keys)
+        else
+          value
         end
       end
+      private :deep_key_or_nil
     end
 
     def initialize(name)

data/lib/ncs_navigator/mdes/version.rb

@@ -1,5 +1,5 @@
 module NcsNavigator
   module Mdes
-    VERSION = '0.12.0'
+    VERSION = '0.13.0'
   end
 end

data/ncs_mdes.gemspec

@@ -19,7 +19,7 @@ National Children's Study's Master Data Element Specification.
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
 
-  s.add_dependency 'nokogiri', '~> 1.5.6'
+  s.add_dependency 'nokogiri', '~> 1.5.7'
 
   s.add_development_dependency 'rspec', '~> 2.6.0' # Can't use 2.7.0 due to #477
   s.add_development_dependency 'rake', '~> 0.9.2'

data/spec/ncs_navigator/mdes/source_documents_spec.rb

@@ -200,6 +200,20 @@ module NcsNavigator::Mdes
         end
       end
 
+      describe '3.3' do
+        let(:version) { '3.3' }
+
+        include_context 'version docs'
+
+        it 'has the correct path for the schema' do
+          subject.schema.should =~ %r{3.3/NCS_Transmission_Schema_3.3.00.00.xsd$}
+        end
+
+        it 'has a different specification_version' do
+          subject.specification_version.should == '3.3.00.00'
+        end
+      end
+
       it 'fails for an unsupported version' do
         lambda { SourceDocuments.get('1.0') }.
           should raise_error('MDES 1.0 is not supported by this version of ncs_mdes')

data/spec/ncs_navigator/mdes/specification_spec.rb

@@ -31,6 +31,17 @@ module NcsNavigator::Mdes
           should be_a TransmissionTable
       end
 
+      it 'passes down heuristic overrides' do
+        spec = Specification.new('2.0', :log => logger)
+
+        TransmissionTable.should_receive(:from_element).
+          with(anything, include(:heuristic_overrides => spec.heuristic_overrides)).
+          at_least(:once).
+          and_return(TransmissionTable.new('mocked'))
+
+        spec.transmission_tables # force parsing
+      end
+
       shared_examples 'tables fully resolved' do
         let!(:tables) { Specification.new(version, :log => logger).transmission_tables }
 
@@ -65,6 +76,18 @@ module NcsNavigator::Mdes
           index = tables.each_with_object(Hash.new(0)) { |t, acc| acc[t.child_instrument_table?] += 1 }
           index.keys.sort_by { |k| k.inspect }.should == [false, nil, true]
         end
+
+        it 'has a primary key for every table' do
+          no_pk_tables = tables.select { |table| table.primary_key_variables.empty? }
+
+          no_pk_tables.should == []
+        end
+
+        it 'has no multi-column primary keys' do
+          multi_column_key_tables = tables.select { |table| table.primary_key_variables.size > 1 }
+
+          multi_column_key_tables.should == []
+        end
       end
 
       context 'in version 1.2' do
@@ -115,6 +138,13 @@ module NcsNavigator::Mdes
 
         include_examples 'tables fully resolved'
       end
+
+      context 'in version 3.3' do
+        let(:version) { '3.3' }
+        let(:expected_table_count) { 668 }
+
+        include_examples 'tables fully resolved'
+      end
     end
 
     describe '#specification_version' do
@@ -198,6 +228,14 @@ module NcsNavigator::Mdes
           disposition_codes.size.should == 332
         end
       end
+
+      context 'in version 3.3' do
+        let(:disposition_codes) { Specification.new('3.3', :log => logger).disposition_codes }
+
+        it 'has 332 codes' do
+          disposition_codes.size.should == 332
+        end
+      end
     end
 
     describe '#[]' do
@@ -226,6 +264,17 @@ module NcsNavigator::Mdes
           should be_a VariableType
       end
 
+      it 'passes down heuristic overrides when parsing' do
+        spec = Specification.new('2.0', :log => logger)
+
+        VariableType.should_receive(:from_xsd_simple_type).
+          with(anything, include(:heuristic_overrides => spec.heuristic_overrides)).
+          at_least(:once).
+          and_return(VariableType.new('mocked'))
+
+        spec.types # force parsing
+      end
+
       shared_examples 'types fully resolved' do
         let!(:types) { Specification.new(version, :log => logger).types }
 
@@ -286,6 +335,13 @@ module NcsNavigator::Mdes
 
         include_examples 'types fully resolved'
       end
+
+      context 'version 3.3' do
+        let(:version) { '3.3' }
+        let(:expected_type_count) { 656 }
+
+        include_examples 'types fully resolved'
+      end
     end
 
     describe '#diff' do

data/spec/ncs_navigator/mdes/transmission_table_spec.rb

@@ -46,7 +46,8 @@ module NcsNavigator::Mdes
 XSD
       }
 
-      subject { TransmissionTable.from_element(element) }
+      subject { TransmissionTable.from_element(element, options) }
+      let(:options) { { } }
 
       it 'has the right name' do
         subject.name.should == 'study_center'
@@ -56,6 +57,29 @@ XSD
         subject.variables.collect(&:name).
           should == %w(sc_id sc_name comments transaction_type)
       end
+
+      it 'sends the current table name when constructing variables' do
+        Variable.should_receive(:from_element).
+          with(anything, include(:current_table_name => 'study_center')).
+          at_least(:once)
+
+        subject # to force parsing
+      end
+
+      it 'does not leak the current table name to the outer options hash' do
+        subject # to force parsing
+        options.should_not have_key(:current_table_name)
+      end
+
+      it 'passes down provided options when constructing variables' do
+        options[:foo] = 'bar'
+
+        Variable.should_receive(:from_element).
+          with(anything, include(:foo => 'bar')).
+          at_least(:once)
+
+        subject # to force parsing
+      end
     end
 
     describe '#initialize' do
@@ -256,5 +280,58 @@ XSD
         end
       end
     end
+
+    describe '#primary_key_variables' do
+      def table_with_typed_variables(table_name, variables_and_types)
+          TransmissionTable.new(table_name).tap do |t|
+            t.variables = variables_and_types.collect do |vn, type|
+              Variable.new(vn).tap do |v|
+                v.type = VariableType.new(type)
+              end
+            end
+          end
+      end
+
+      describe 'for a regular table' do
+        let(:table) {
+          table_with_typed_variables('example',
+            'foo' => 'primaryKeyType',
+            'bar' => 'primaryKeyType',
+            'baz' => 'foreignKeyTypeRequired',
+          )
+        }
+
+        it 'finds all the variables with the PK type' do
+          table.primary_key_variables.collect(&:name).should == %w(foo bar)
+        end
+      end
+
+      describe 'for psu' do
+        let(:psu_table) {
+          table_with_typed_variables('psu',
+            'sc_id' => 'study_center_cl1',
+            'psu_id' => 'psu_cl1',
+            'psu_name' => nil,
+          )
+        }
+
+        it 'finds the PK' do
+          psu_table.primary_key_variables.collect(&:name).should == ['psu_id']
+        end
+      end
+
+      describe 'for study_center' do
+        let(:sc_table) {
+          table_with_typed_variables('study_center',
+            'sc_id' => 'study_center_cl1',
+            'sc_name' => nil,
+          )
+        }
+
+        it 'finds the PK' do
+          sc_table.primary_key_variables.collect(&:name).should == ['sc_id']
+        end
+      end
+    end
   end
 end

data/spec/ncs_navigator/mdes/variable_spec.rb

@@ -5,8 +5,8 @@ require 'nokogiri'
 module NcsNavigator::Mdes
   describe Variable do
     describe '.from_element' do
-      def variable(s)
-        Variable.from_element(schema_element(s), :log => logger)
+      def variable(s, options={})
+        Variable.from_element(schema_element(s), { :log => logger }.merge(options))
       end
 
       let(:comments) {
@@ -74,6 +74,61 @@ XSD
               sc_id.type.should be_reference
             end
           end
+
+          context 'with an override' do
+            let(:options) {
+              {
+                :heuristic_overrides => {
+                  'variable_type_references' => {
+                    overridden_table_name => {
+                      'not_a_pk' => override_type
+                    }
+                  }
+                },
+                :current_table_name => overridden_table_name
+              }
+            }
+
+            let(:overridden_table_name) { 'link_whatever' }
+            let(:type_in_xsd) { 'ncs:primaryKeyType' }
+            let(:override_type) { 'ncs:foreignKeyTypeRequired' }
+
+            let(:subject) {
+              variable("<xs:element name='not_a_pk' type='#{type_in_xsd}'/>", options)
+            }
+
+            it 'uses an override which matches' do
+              subject.type.name.should == 'ncs:foreignKeyTypeRequired'
+            end
+
+            it 'does not use an override which does not match by table name' do
+              options[:current_table_name] = 'another_table'
+
+              subject.type.name.should == type_in_xsd
+            end
+
+            it 'does not use an override which does not match by variable name' do
+              options[:heuristic_overrides]['variable_type_references']['link_whatever'] = {
+                'another_overridden_variable' => 'xs:integer'
+              }
+
+              subject.type.name.should == type_in_xsd
+            end
+
+            context 'when the override is an schema type' do
+              let(:override_type) { 'xs:integer' }
+
+              it 'treats extracts the XSD type' do
+                subject.type.base_type.should == :integer
+              end
+            end
+
+            context 'when the override is an internal reference' do
+              it 'is a reference' do
+                subject.type.should be_reference
+              end
+            end
+          end
         end
 
         context 'when none present' do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ncs_mdes
 version: !ruby/object:Gem::Version
-  version: 0.12.0
+  version: 0.13.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-03-12 00:00:00.000000000 Z
+date: 2013-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -18,7 +18,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.5.6
+        version: 1.5.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.5.6
+        version: 1.5.7
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -148,6 +148,11 @@ files:
 - documents/3.2/disposition_codes.yml
 - documents/3.2/extract_disposition_codes.rb
 - documents/3.2/heuristic_overrides.yml
+- documents/3.3/NCS_Transmission_Schema_3.3.00.00.xsd
+- documents/3.3/child_or_parent_instrument_tables.yml
+- documents/3.3/disposition_codes.yml
+- documents/3.3/extract_disposition_codes.rb
+- documents/3.3/heuristic_overrides.yml
 - documents/scan_p_ids_for_children.rb
 - lib/ncs_navigator/mdes.rb
 - lib/ncs_navigator/mdes/code_list.rb
@@ -190,7 +195,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1618062826933135286
+      hash: 2077666531396508902
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -199,7 +204,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1618062826933135286
+      hash: 2077666531396508902
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.25